When I did the infusion, I expected the pearl to degrade a tier, but it seems the entire pearl got consumed in a creative world. I my survival world, it did work just fine. Something is weird.

Do you mean that in creative mode, the morphic tool/armour recipe consumed a full pearl, and in survival mode only a portion of the pearl was consumed? Furthermore, what was the durability of the pearl in each case (full, nodule or mote)?

So looking at the code it does look like I messed up and didn't account for the pearl. I'll have to check the TC code later to see what might cause it to work only sometimes. Curiously, it did seem to work for me throughout testing, so maybe there's a case I missed.

Also, what other TC addons do you have installed, if any?

Now that you mention, it's possibly/likely due to ThaumTweaks; it adds a crafting recipe to combine weaker pearls to restore durability.

Ouch, I just learned my entire pearl was consumed during a morphic tool infusion. In survival. Thankfully I can get more easily, I'm finally at a point where I can, but that definitely hurt a bit.

This is 100% my fault and has nothing to do with ThaumTweaks, sorry about that